Molecular docking study of new sorafenib analogues as platelet-derived growth factor receptor inhibitors for the treatment of cancer by Marwan I Jihad, Monther F Mahdi

“…A high-definition X-ray crystallography of the platelet-derived growth factor protein [Protein Data Bank (PDB) ID 6JOL] was downloaded from the website PDB with a resolution of 2 A. …”
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Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment by Dariusz Mrozek, Tomasz Dąbek, Bożena Małysiak-Mrozek

“…Calculation of structural features of proteins, nucleic acids, and nucleic acid-protein complexes on the basis of their geometries and studying various interactions within these macromolecules, for which high-resolution structures are stored in Protein Data Bank (PDB), require parsing and extraction of suitable data stored in text files. …”
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NOE distance and dihedral angle restraints to calculate the solution structure of the NDH-1 complex subunit CupS from Thermosynechococcus elongatus by Annika Korste, Hannes Wulfhorst, Takahisa Ikegami, Marc M. Nowaczyk, Raphael Stoll

“…These restraints to calculate the structure in solution of CupS have been deposited to the Protein Data Bank (www.rcsb.org) under PDB-ID accession number 2MXA. …”
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Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate. by Keith Lange, Kathleen M Frey, Tyler Eck, Cheryl A Janson, Ueli Gubler, Nina M Goodey

“…The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. …”
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The interaction between amyloid-β peptides and anionic lipid membranes containing cholesterol and melatonin. by Hannah Dies, Laura Toppozini, Maikel C Rheinstädter

“…We compare the experimentally determined electron densities in the gel state of the membranes with density calculations from peptide structures reported in the Protein Data Bank in order to determine the position of the peptide in the bilayers. …”
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Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins by Farideh Halakou, Emel Sen Kilic, Engin Cukuroglu, Ozlem Keskin, Attila Gursoy

“…Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. …”
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Pembuatan Protokol Penapisan Virtual Berbasis Stuktur (pvbs) untuk Identifikasi Ligan Inhibitor Reseptor Platelet-Activating Factor (PAF-r) sebagai Target Terapeutik Asma menggunak... by Gerry Nugraha, Enade Perdana Istyastono

“…Research in building structure-based virtual screening protocol (SBVS) for identification of PAF-r ligand inhibitors has been performed, the receptor crystal structure was obtained from the Protein Data Bank (PDB ID: 5zkp), while the ligand used as a leading compound is Y-24180, obtained from U.S. …”
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Identification of putative domain linkers by a neural network – application to a large sequence database by Kuroda Yutaka, Miyazaki Satoshi, Yokoyama Shigeyuki

“…</p> <p>Results</p> <p>Our search detected 3009 putative domain linkers adjacent to or overlapping with domains, as defined by sequence similarity to either Protein Data Bank (PDB) or Conserved Domain Database (CDD) sequences. …”
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LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction by Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara, Daisuke Kihara

“…While the number of known structures deposited in the Protein Data Bank is increasing, there are still many cases where the structures of individual proteins that users want to dock are not determined yet. …”
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Serine racemase interaction with N-methyl-D-aspartate receptors antagonist reveals potential alternative target of chronic pain treatment: Molecular docking study by Ristiawan Muji Laksono, Handono Kalim, Mohammad Saifur Rohman, Nashi Widodo, Muhammad Ramli Ahmad

“…The SR structure was obtained from Protein data bank (PDB) (3l6B) and then docked with ligands using the AutoDock Vina. …”
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Binding mode information improves fragment docking by Célien Jacquemard, Malgorzata N. Drwal, Jérémy Desaphy, Esther Kellenberger

“…We prepared a test set composed of high-quality structures of the Protein Data Bank. We generated and evaluated the docking poses of 586 fragment/protein complexes. …”
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Computational Prediction and Experimental Validation of the Unique Molecular Mode of Action of Scoulerine by Mahshad Moshari, Qian Wang, Marek Michalak, Mariusz Klobukowski, Jack Adam Tuszynski

“…Based on the existing data in the Protein Data Bank (PDB) and using homology modeling, we create human tubulin structures corresponding to both free tubulin dimers and tubulin in a microtubule. …”
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A Simple Comparison between Specific Protein Secondary Structure Prediction Tools by TJ Koswatta, P Samaraweera, VA Sumanasinghe

“…Secondary structure data of ten proteins containing 190 secondary structure motifs were collected from Protein Data Bank (PDB). The amino acid sequences of the proteins were then evaluated using GOR, PSIPRED, HNN, PROF, and YASPIN secondary structure prediction tools and the results were compared with the structural information obtained from PDB. …”
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The Southern European Atlantic Diet and Its Supplements: The Chemical Bases of Its Anticancer Properties by Pablo García Vivanco, Pablo Taboada, Alberto Coelho

“…The information sources consulted, complemented by crystallographic data from the Protein Data Bank, establish a direct link between the SEAD and its anticancer properties. …”
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Crystallography and Databases by Ian Bruno, Saulius Gražulis, John R Helliwell, Soorya N Kabekkodu, Brian McMahon, John Westbrook

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Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins by Elisia A. Paiz, Karen A. Lewis, Steven T. Whitten

“…The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. …”
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A distance geometry-based description and validation of protein main-chain conformation by Joana Pereira, Victor S. Lamzin

“…These were computed for ∼1.3 million dipeptide units collected from nonredundant good-quality structures in the Protein Data Bank and subjected to principal component analysis. …”
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Protein homodimers structure prediction based on deep neural network by A. Y. Hadarovich, A. A. Kalinouski, A. V. Tuzikov

“…The suggested approach was tested and validated on a dataset of protein homodimers from Protein Data Bank (PDB). The developed procedure could be also used for evaluating protein homodimer models as one of the stages in drug compounds developing.…”
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Mathematical topology and geometry-based classification of tauopathies by Masumi Sugiyama, Kenneth S. Kosik, Eleni Panagiotou

“…In this manuscript, we employ for the first time mathematical topology and geometry to classify neurodegenerative diseases by using cryo-electron microscopy structures of tau filaments that are available in the Protein Data Bank. By employing mathematical topology metrics (Gauss linking integral, writhe and second Vassiliev measure) we achieve a consistent, but more refined classification of tauopathies, than what was previously observed through visual inspection. …”
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Mimetismo molecular entre el Plasmodium sp y los antígenos del síndrome de Guillain-Barre by Yuliana Marcela Emiliani Navarro, D Vega, G Muzi, Marlon Munera-Gomez, Andrés Sánchez

“…Métodos: Se emplearon PSI-Blast, Praline, Emboss, Protein Data Bank, Swiss Model Server, AlphaFold 2, Ellipro y PyMol 2.3 para buscar homologías, realizar alineamientos, obtener estructuras proteicas y predecir epítopos. …”
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